if ncs_object:
n_ops = max(1, ncs_object.max_operators())
else:
n_ops = 1
# Get sequence if extract_unique is set
sequence = None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence
remove_duplicates = True
else:
remove_duplicates = False
from iotbx.bioinformatics import get_sequences
sequence = (" ".join(
get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if params.chain_type in ['None', None]: params.chain_type = None
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None, 'PROTEIN']:
n_protein = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='PROTEIN'))
else:
n_protein = 0
if params.chain_type in [None, 'RNA']:
n_rna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='RNA'))
def run(args,
crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if (log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message = """\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:""" % h
if (len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args=args,
cmd_cs=crystal_symmetry,
master_params=master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds = lower_bounds
if upper_bounds:
params.upper_bounds = upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names = [params.pdb_file]
if (len(inputs.pdb_file_names) != 1 and not params.density_select
and not pdb_hierarchy and not params.keep_map_size
and not params.upper_bounds and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, " +
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names) > 0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy = None
# Map or map coefficients
map_coeff = None
if (not map_data):
# read first mtz file
if ((len(inputs.reflection_file_names) > 0)
or (params.map_coefficients_file is not None)):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(
params.map_coefficients_file)
else:
inputs.reflection_file_names[
0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name=inputs.reflection_file_names[0],
label=params.label,
type="complex",
log=log)
if not crystal_symmetry:
crystal_symmetry = map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(
resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix = os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ((inputs.ccp4_map is not None)
or (params.ccp4_map_file is not None)):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ", out=log)
if not crystal_symmetry:
crystal_symmetry = ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix = os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix = None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry = crystal_symmetry
# final check that map_data exists
if (map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names) > 0:
output_prefix = os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix = map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy = iotbx.pdb.input(
source_info='', lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string=params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'" % params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(radius=params.selection_radius,
selection=selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object = ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file, log=log)
print >> log, "Total of %s operators read" % (
ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators() < 1:
print >> log, "No symmetry available"
if ncs_object:
n_ops = max(1, ncs_object.max_operators())
else:
n_ops = 1
# Get sequence if extract_unique is set
sequence = None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates = True
else:
remove_duplicates = False
from iotbx.bioinformatics import get_sequences
sequence = n_ops * (" ".join(
get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None, 'PROTEIN']:
n_protein = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='PROTEIN'))
else:
n_protein = 0
if params.chain_type in [None, 'RNA']:
n_rna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='RNA'))
else:
n_rna = 0
if params.chain_type in [None, 'DNA']:
n_dna = len(
text_from_chains_matching_chain_type(text=sequence,
chain_type='DNA'))
else:
n_dna = 0
params.molecular_mass = n_protein * 110 + (n_rna + n_dna) * 330
elif not params.molecular_mass:
raise Sorry(
"Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass = None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files",
out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files",
out=log)
#
if params.value_outside_atoms == 'mean':
print >> log, "\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >> log, "\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size() > 0:
print >> log, "\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >> log, "\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >> log, "\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >> log, "Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" % (
tuple(list(params.lower_bounds) + list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure=xray_structure,
map_data=map_data.as_double(),
box_cushion=params.box_cushion,
selection=selection,
density_select=params.density_select,
threshold=params.density_select_threshold,
get_half_height_width=params.get_half_height_width,
mask_atoms=params.mask_atoms,
soft_mask=params.soft_mask,
soft_mask_radius=params.soft_mask_radius,
mask_atoms_atom_radius=params.mask_atoms_atom_radius,
value_outside_atoms=params.value_outside_atoms,
keep_map_size=params.keep_map_size,
restrict_map_size=params.restrict_map_size,
lower_bounds=params.lower_bounds,
upper_bounds=params.upper_bounds,
extract_unique=params.extract_unique,
chain_type=params.chain_type,
sequence=sequence,
solvent_content=params.solvent_content,
molecular_mass=params.molecular_mass,
resolution=params.resolution,
ncs_object=ncs_object,
symmetry=params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy = ph_box
if (inputs and inputs.crystal_symmetry and inputs.ccp4_map
and inputs.crystal_symmetry.unit_cell().parameters()
and inputs.ccp4_map.unit_cell_parameters) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >> log, "\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map = inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map = None
box.unit_cell_parameters_deduced_from_map_grid = None
# ncs_object is original
# box.ncs_object is shifted by shift_cart
print >> log, "Box cell dimensions: (%.2f, %.2f, %.2f) A" % (
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if params.keep_origin:
print >> log, "Box origin is at grid position of : (%d, %d, %d) " % (
tuple(box.origin_shift_grid_units(reverse=True)))
print >> log, "Box origin is at coordinates: (%.2f, %.2f, %.2f) A" % (
tuple(-col(box.shift_cart)))
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
if (not params.keep_origin):
if box.shift_cart:
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A" %(
tuple(box.shift_cart))
else:
print >>log,"\nOutput files are in same location as original: origin "+\
"is at (0,0,0)"
else: # keep_origin
print >> log, "\nOutput files are in same location as original, just cut out."
print >> log, "Note that output maps are only valid in the cut out region.\n"
if params.keep_origin:
ph_box_original_location = ph_box.deep_copy()
sites_cart = box.shift_sites_cart_back(
box.xray_structure_box.sites_cart())
xrs_offset = ph_box_original_location.extract_xray_structure(
crystal_symmetry=box.xray_structure_box.crystal_symmetry(
)).replace_sites_cart(new_sites=sites_cart)
ph_box_original_location.adopt_xray_structure(xrs_offset)
box.hierarchy_original_location = ph_box_original_location
else:
box.hierarchy_original_location = None
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues > 0:
if (params.output_file_name_prefix is None):
file_name = "%s_box.pdb" % output_prefix
else:
file_name = "%s.pdb" % params.output_file_name_prefix
if params.keep_origin: # Keeping origin
print >> log, "Writing boxed PDB with box unit cell and in "+\
"original\n position to: %s"%(
file_name)
ph_box_original_location.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
else: # write box PDB in box cell
print >> log, "Writing shifted boxed PDB to file: %s" % file_name
ph_box.write_pdb_file(
file_name=file_name,
crystal_symmetry=box.xray_structure_box.crystal_symmetry())
# Write NCS file if NCS
if ncs_object and ncs_object.max_operators() > 0:
if (params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec" % output_prefix
else:
output_symmetry_file = "%s.ncs_spec" % params.output_file_name_prefix
if params.keep_origin:
if params.symmetry_file:
print >> log, "\nDuplicating symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
else:
print >> log, "\nWriting symmetry to %s" % (
output_symmetry_file)
ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
else:
print >> log, "\nOffsetting symmetry in %s and writing to %s" % (
params.symmetry_file, output_symmetry_file)
box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
# Write ccp4 map. Shift back to original location if keep_origin=True
if ("ccp4" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.ccp4" % output_prefix
else:
file_name = "%s.ccp4" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and "+\
"original\n position to CCP4 formatted file: %s"%file_name
else:
print >> log, "Writing box map shifted to (0,0,0) to CCP4 "+\
"formatted file: %s"%file_name
box.write_ccp4_map(file_name=file_name,
shift_back=params.keep_origin)
# Write xplor map. Shift back if keep_origin=True
if ("xplor" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.xplor" % output_prefix
else:
file_name = "%s.xplor" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing boxed map with box unit_cell and original "+\
"position\n to X-plor formatted file: %s"%file_name
else:
print >> log, "Writing box_map shifted to (0,0,0) to X-plor "+\
"formatted file: %s"%file_name
box.write_xplor_map(file_name=file_name,
shift_back=params.keep_origin)
# Write mtz map coeffs. Shift back if keep_origin=True
if ("mtz" in params.output_format):
if (params.output_file_name_prefix is None):
file_name = "%s_box.mtz" % output_prefix
else:
file_name = "%s.mtz" % params.output_file_name_prefix
if params.keep_origin:
print >> log, "Writing map coefficients with box_map unit_cell"+\
" but position matching\n "+\
" original position to MTZ file: %s"%file_name
else:
print >> log, "Writing box_map coefficients shifted to (0,0,0) "+\
"to MTZ file: %s"%file_name
if (map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(
map_data=box.map_box,
unit_cell=box.xray_structure_box.unit_cell())
box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor,
file_name=file_name,
shift_back=params.keep_origin)
print >> log
return box
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
mask_data=None,
half_map_data_list=None,
half_map_labels_list=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print(default_message)
master_phil.show(prefix=" ")
return
# Process inputs ignoring symmetry conflicts just to get the value of
# ignore_symmetry_conflicts...
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=True)
params = inputs.params.extract()
# Now process inputs for real and write a nice error message if necessary.
try:
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil,
suppress_symmetry_related_errors=params.ignore_symmetry_conflicts)
except Exception as e:
if str(e).find("symmetry mismatch ")>1:
raise Sorry(str(e)+"\nTry 'ignore_symmetry_conflicts=True'")
else:
raise e
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
params.mask_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique and not params.bounds_match_this_file):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, mask_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms )):
raise Sorry("PDB file is needed for mask_atoms")
if params.soft_mask and (not params.resolution) and \
(len(inputs.pdb_file_names)!=1 and not pdb_hierarchy):
raise Sorry("Need resolution for soft_mask without PDB file")
if ((params.density_select or params.mask_select) and params.keep_map_size):
raise Sorry("Cannot set both density_select/mask_select and keep_map_size")
if ((params.density_select or params.mask_select) and params.upper_bounds):
raise Sorry("Cannot set both density_select/mask_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique):
if (not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (not params.symmetry) and (not params.symmetry_file) and \
(not ncs_object):
raise Sorry(
"Please supply a symmetry file or symmetry for extract_unique (you "+
"\ncan try symmetry=ALL if you do not know your symmetry or "+
"symmetry=C1 if \nthere is none)")
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
ncs_object.set_unit_ncs()
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
print("\nNOTE: Skipping write of mtz file as keep_origin=True and \n"+\
"keep_map_size is False\n")
params.output_format=remove_element(params.output_format,element='mtz')
if (write_output_files) and ("mtz" in params.output_format) and (
(params.extract_unique)):
print("\nNOTE: Skipping write of mtz file as extract_unique=True\n")
params.output_format=remove_element(params.output_format,element='mtz')
if params.output_origin_match_this_file or params.bounds_match_this_file:
if params.output_origin_match_this_file:
fn=params.output_origin_match_this_file
if params.bounds_match_this_file:
raise Sorry("Cannot match origin and bounds at same time")
else:
fn=params.bounds_match_this_file
if not params.ccp4_map_file:
raise Sorry(
"Need to specify your input file with ccp4_map_file=xxx if you use "+
"output_origin_match_this_file=xxxx or bounds_match_this_file=xxxx")
af = any_file(fn)
if (af.file_type == 'ccp4_map'):
origin=af.file_content.data.origin()
if params.output_origin_match_this_file:
params.output_origin_grid_units=origin
print("Origin of (%s,%s,%s) taken from %s" %(
origin[0],origin[1],origin[2],fn))
else:
all=af.file_content.data.all()
params.lower_bounds=origin
print("Lower bounds of (%s,%s,%s) taken from %s" %(
params.lower_bounds[0],params.lower_bounds[1],
params.lower_bounds[2],fn))
params.upper_bounds=list(col(origin)+col(all)-col((1,1,1)))
print("upper bounds of (%s,%s,%s) taken from %s" %(
params.upper_bounds[0],params.upper_bounds[1],
params.upper_bounds[2],fn))
params.bounds_are_absolute=True
else:
raise Sorry("Unable to interpret %s as map file" %(fn))
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print("Setting keep_origin=False as output_origin_grid_units is set")
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
input_map_labels=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
input_map_labels=ccp4_map.get_labels()
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.half_map_list and (not half_map_data_list):
if not params.extract_unique:
raise Sorry("Can only use half_map_with extract_unique")
print ("Reading half-maps",params.half_map_list)
half_map_data_list=[]
half_map_labels_list=[]
for fn in params.half_map_list:
print("Reading half map from %s" %(fn),file=log)
af = any_file(fn)
print_statistics.make_sub_header("CCP4 map", out=log)
h_ccp4_map = af.file_content
h_ccp4_map.show_summary(prefix=" ",out=log)
h_map_data = h_ccp4_map.data
half_map_data_list.append(h_map_data)
half_map_labels_list.append(h_ccp4_map.get_labels())
if params.map_scale_factor:
print("Applying scale factor of %s to map data on read-in" %(
params.map_scale_factor))
map_data=map_data*params.map_scale_factor
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
if not params.selection: params.selection="all"
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print("Selection string: selection='%s'"%params.selection, file=log)
print(" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size()), file=log)
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print("Total of %s operators read" %(ncs_object.max_operators()), file=log)
if not ncs_object or ncs_object.max_operators()<1:
print("No symmetry available", file=log)
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique or params.mask_select:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=(" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if params.chain_type in ['None',None]: params.chain_type=None
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_ops*(n_protein*110+(n_rna+n_dna)*330)
print("\nEstimate of molecular mass is %.0f " %(params.molecular_mass), file=log)
if params.density_select or params.mask_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print("\nValue outside atoms mask will be set to mean inside mask", file=log)
if params.get_half_height_width and params.density_select:
print("\nHalf width at half height will be used to id boundaries", file=log)
if params.soft_mask and sites_cart_all.size()>0:
print("\nSoft mask will be applied to model-based mask", file=log)
elif params.soft_mask:
print ("\nSoft mask will be applied to outside of map box",file=log)
if params.keep_map_size:
print("\nEntire map will be kept (not cutting out region)", file=log)
if params.restrict_map_size:
print("\nOutput map will be within input map", file=log)
if params.lower_bounds and params.upper_bounds:
print("Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds))), file=log)
if mask_data:
mask_data=mask_data.as_double()
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
mask_data = mask_data,
box_cushion = params.box_cushion,
selection = selection,
mask_select = params.mask_select,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
bounds_are_absolute = params.bounds_are_absolute,
zero_outside_original_map = params.zero_outside_original_map,
extract_unique = params.extract_unique,
target_ncs_au_file = params.target_ncs_au_file,
regions_to_keep = params.regions_to_keep,
box_buffer = params.box_buffer,
soft_mask_extract_unique = params.soft_mask_extract_unique,
mask_expand_ratio = params.mask_expand_ratio,
keep_low_density = params.keep_low_density,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
half_map_data_list = half_map_data_list,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if params.mask_select:
print("\nSolvent content used in mask_select: %.3f " %(
box.get_solvent_content()),file=log)
if (inputs and
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print("\nNOTE: Input CCP4 map is only part of unit cell:", file=log)
print("Full unit cell ('unit cell parameters'): "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.ccp4_map.unit_cell_parameters), file=log)
print("Size of CCP4 map 'map unit cell': "+\
"(%.1f, %.1f, %.1f, %.1f, %.1f, %.1f) A" %tuple(
inputs.crystal_symmetry.unit_cell().parameters()), file=log)
print("Full unit cell as grid units: (%s, %s, %s)" %(
inputs.ccp4_map.unit_cell_grid), file=log)
print("Map unit cell as grid units: (%s, %s, %s)" %(
map_data.all()), file=log)
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print(box.pdb_outside_box_msg, file=log)
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print("\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3]), file=log)
if box.shift_cart:
print("Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart))), file=log)
if (params.keep_origin):
print("\nRestoring original position for output files", file=log)
print("Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True))), file=log)
print("\nOutput files will be in same location as original", end=' ', file=log)
if not params.keep_map_size:
print("just cut out.", file=log)
else:
print("keeping entire map", file=log)
print("Note that output maps are only valid in the cut out region.\n", file=log)
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print("Output map origin to be shifted to match target", file=log)
print("Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print("Final origin will be at (0,0,0)", file=log)
print("Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart))), file=log)
else:
print("\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n", file=log)
print("\nBox grid: (%s, %s, %s) " %(output_box.map_box.all()),file=log)
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print("Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file", file=log)
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print("Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters()), file=log)
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print("Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid), file=log)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print("WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing)), file=log)
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print("Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters())), file=log)
else:
output_unit_cell_grid = output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print("Writing boxed PDB with box unit cell to %s" %(
file_name), file=log)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print("\nWriting symmetry to %s" %( output_symmetry_file), file=log)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
from iotbx.mrcfile import create_output_labels
if params.extract_unique:
program_name='map_box using extract_unique'
limitations=["extract_unique"]
else:
program_name='map_box'
limitations=[]
labels=create_output_labels(program_name=program_name,
input_file_name=inputs.ccp4_map_file_name,
input_labels=input_map_labels,
limitations=limitations,
output_labels=params.output_map_labels)
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print("Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name, file=log)
if not params.half_map_list:
params.half_map_list=[]
if not output_box.map_box_half_map_list:
output_box.map_box_half_map_list=[]
if not half_map_labels_list:
half_map_labels_list=len(output_box.map_box_half_map_list)*[None]
for hm,labels,fn in zip(
output_box.map_box_half_map_list,
half_map_labels_list,
params.half_map_list): # half maps matching
labels=create_output_labels(program_name=program_name,
input_file_name=fn,
input_labels=labels,
limitations=limitations,
output_labels=params.output_map_labels)
hm_fn="%s_box.ccp4" %( ".".join(os.path.basename(fn).split(".")[:-1]))
output_box.write_ccp4_map(file_name=hm_fn,
map_data=hm,
output_crystal_symmetry=output_crystal_symmetry,
output_mean=params.output_ccp4_map_mean,
output_sd=params.output_ccp4_map_sd,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,
output_map_labels=labels,
output_external_origin=params.output_external_origin)
print ("Writing boxed half map to: %s " %(hm_fn),file=log)
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print("Writing boxed map "+\
"to X-plor formatted file: %s"%file_name, file=log)
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print("Writing map coefficients "+\
"to MTZ file: %s"%file_name, file=log)
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
scale_max=params.scale_max,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print(file=log)
return box
def run(args, crystal_symmetry=None,
ncs_object=None,
pdb_hierarchy=None,
map_data=None,
lower_bounds=None,
upper_bounds=None,
write_output_files=True,
log=None):
h = "phenix.map_box: extract box with model and map around selected atoms"
if(log is None): log = sys.stdout
print_statistics.make_header(h, out=log)
default_message="""\
%s.
Usage:
phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"
or
phenix.map_box map.ccp4 density_select=True
Parameters:"""%h
if(len(args) == 0 and not pdb_hierarchy):
print default_message
master_phil.show(prefix=" ")
return
inputs = mmtbx.utils.process_command_line_args(args = args,
cmd_cs=crystal_symmetry,
master_params = master_phil)
params = inputs.params.extract()
master_phil.format(python_object=params).show(out=log)
# Overwrite params with parameters in call if available
if lower_bounds:
params.lower_bounds=lower_bounds
if upper_bounds:
params.upper_bounds=upper_bounds
# PDB file
if params.pdb_file and not inputs.pdb_file_names and not pdb_hierarchy:
inputs.pdb_file_names=[params.pdb_file]
if(len(inputs.pdb_file_names)!=1 and not params.density_select and not
pdb_hierarchy and not params.keep_map_size and not params.upper_bounds
and not params.extract_unique):
raise Sorry("PDB file is needed unless extract_unique, "+
"density_select, keep_map_size \nor bounds are set .")
if (len(inputs.pdb_file_names)!=1 and not pdb_hierarchy and \
(params.mask_atoms or params.soft_mask )):
raise Sorry("PDB file is needed for mask_atoms or soft_mask")
if (params.density_select and params.keep_map_size):
raise Sorry("Cannot set both density_select and keep_map_size")
if (params.density_select and params.upper_bounds):
raise Sorry("Cannot set both density_select and bounds")
if (params.keep_map_size and params.upper_bounds):
raise Sorry("Cannot set both keep_map_size and bounds")
if (params.upper_bounds and not params.lower_bounds):
raise Sorry("Please set lower_bounds if you set upper_bounds")
if (params.extract_unique and not params.resolution):
raise Sorry("Please set resolution for extract_unique")
if (write_output_files) and ("mtz" in params.output_format) and (
(params.keep_origin) and (not params.keep_map_size)):
raise Sorry("Please set output_format=ccp4 to skip mtz or set "+\
"keep_origin=False or keep_map_size=True")
if params.keep_input_unit_cell_and_grid and (
(params.output_unit_cell_grid is not None ) or
(params.output_unit_cell is not None ) ):
raise Sorry("If you set keep_input_unit_cell_and_grid then you cannot "+\
"set \noutput_unit_cell_grid or output_unit_cell")
if params.output_origin_grid_units is not None and params.keep_origin:
params.keep_origin=False
print "Setting keep_origin=False as output_origin_grid_units is set"
print_statistics.make_sub_header("pdb model", out=log)
if len(inputs.pdb_file_names)>0:
pdb_inp = iotbx.pdb.input(file_name=inputs.pdb_file_names[0])
pdb_hierarchy = pdb_inp.construct_hierarchy()
if pdb_hierarchy:
pdb_atoms = pdb_hierarchy.atoms()
pdb_atoms.reset_i_seq()
else:
pdb_hierarchy=None
# Map or map coefficients
map_coeff = None
input_unit_cell_grid=None
input_unit_cell=None
if (not map_data):
# read first mtz file
if ( (len(inputs.reflection_file_names) > 0) or
(params.map_coefficients_file is not None) ):
# file in phil takes precedent
if (params.map_coefficients_file is not None):
if (len(inputs.reflection_file_names) == 0):
inputs.reflection_file_names.append(params.map_coefficients_file)
else:
inputs.reflection_file_names[0] = params.map_coefficients_file
map_coeff = reflection_file_utils.extract_miller_array_from_file(
file_name = inputs.reflection_file_names[0],
label = params.label,
type = "complex",
log = log)
if not crystal_symmetry: crystal_symmetry=map_coeff.crystal_symmetry()
fft_map = map_coeff.fft_map(resolution_factor=params.resolution_factor)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
map_or_map_coeffs_prefix=os.path.basename(
inputs.reflection_file_names[0][:-4])
# or read CCP4 map
elif ( (inputs.ccp4_map is not None) or
(params.ccp4_map_file is not None) ):
if (params.ccp4_map_file is not None):
af = any_file(params.ccp4_map_file)
if (af.file_type == 'ccp4_map'):
inputs.ccp4_map = af.file_content
inputs.ccp4_map_file_name = params.ccp4_map_file
print_statistics.make_sub_header("CCP4 map", out=log)
ccp4_map = inputs.ccp4_map
ccp4_map.show_summary(prefix=" ",out=log)
if not crystal_symmetry: crystal_symmetry=ccp4_map.crystal_symmetry()
map_data = ccp4_map.data #map_data()
input_unit_cell_grid=ccp4_map.unit_cell_grid
input_unit_cell=ccp4_map.unit_cell_parameters
if inputs.ccp4_map_file_name.endswith(".ccp4"):
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-5])
else:
map_or_map_coeffs_prefix=os.path.basename(
inputs.ccp4_map_file_name[:-4])
else: # have map_data
map_or_map_coeffs_prefix=None
if params.output_origin_grid_units is not None:
origin_to_match=tuple(params.output_origin_grid_units)
else:
origin_to_match=None
if origin_to_match:
sc=[]
for x,o,a in zip(crystal_symmetry.unit_cell().parameters()[:3],
origin_to_match,
map_data.all()):
sc.append(-x*o/a)
shift_cart_for_origin_to_match=tuple(sc)
else:
origin_to_match=None
shift_cart_for_origin_to_match=None
if crystal_symmetry and not inputs.crystal_symmetry:
inputs.crystal_symmetry=crystal_symmetry
# final check that map_data exists
if(map_data is None):
raise Sorry("Map or map coefficients file is needed.")
if len(inputs.pdb_file_names)>0:
output_prefix=os.path.basename(inputs.pdb_file_names[0])[:-4]
else:
output_prefix=map_or_map_coeffs_prefix
if not pdb_hierarchy: # get an empty hierarchy
from cctbx.array_family import flex
pdb_hierarchy=iotbx.pdb.input(
source_info='',lines=flex.split_lines('')).construct_hierarchy()
xray_structure = pdb_hierarchy.extract_xray_structure(
crystal_symmetry=inputs.crystal_symmetry)
xray_structure.show_summary(f=log)
#
selection = pdb_hierarchy.atom_selection_cache().selection(
string = params.selection)
if selection.size():
print_statistics.make_sub_header("atom selection", out=log)
print >> log, "Selection string: selection='%s'"%params.selection
print >> log, \
" selects %d atoms from total %d atoms."%(selection.count(True),
selection.size())
sites_cart_all = xray_structure.sites_cart()
sites_cart = sites_cart_all.select(selection)
selection = xray_structure.selection_within(
radius = params.selection_radius,
selection = selection)
if not ncs_object:
from mmtbx.ncs.ncs import ncs
ncs_object=ncs()
if params.symmetry_file:
ncs_object.read_ncs(params.symmetry_file,log=log)
print >>log,"Total of %s operators read" %(ncs_object.max_operators())
if not ncs_object or ncs_object.max_operators()<1:
print >>log,"No symmetry available"
if ncs_object:
n_ops=max(1,ncs_object.max_operators())
else:
n_ops=1
# Get sequence if extract_unique is set
sequence=None
if params.extract_unique:
if params.sequence_file:
if n_ops > 1: # get unique part of sequence and multiply
remove_duplicates=True
else:
remove_duplicates=False
from iotbx.bioinformatics import get_sequences
sequence=n_ops * (" ".join(get_sequences(file_name=params.sequence_file,
remove_duplicates=remove_duplicates)))
if sequence and not params.molecular_mass:
# get molecular mass from sequence
from iotbx.bioinformatics import text_from_chains_matching_chain_type
if params.chain_type in [None,'PROTEIN']:
n_protein=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='PROTEIN'))
else:
n_protein=0
if params.chain_type in [None,'RNA']:
n_rna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='RNA'))
else:
n_rna=0
if params.chain_type in [None,'DNA']:
n_dna=len(text_from_chains_matching_chain_type(
text=sequence,chain_type='DNA'))
else:
n_dna=0
params.molecular_mass=n_protein*110+(n_rna+n_dna)*330
elif not params.molecular_mass:
raise Sorry("Need a sequence file or molecular mass for extract_unique")
else:
molecular_mass=None
#
if params.density_select:
print_statistics.make_sub_header(
"Extracting box around selected density and writing output files", out=log)
else:
print_statistics.make_sub_header(
"Extracting box around selected atoms and writing output files", out=log)
#
if params.value_outside_atoms=='mean':
print >>log,"\nValue outside atoms mask will be set to mean inside mask"
if params.get_half_height_width and params.density_select:
print >>log,"\nHalf width at half height will be used to id boundaries"
if params.soft_mask and sites_cart_all.size()>0:
print >>log,"\nSoft mask will be applied to model-based mask"
if params.keep_map_size:
print >>log,"\nEntire map will be kept (not cutting out region)"
if params.restrict_map_size:
print >>log,"\nOutput map will be within input map"
if params.lower_bounds and params.upper_bounds:
print >>log,"Bounds for cut out map are (%s,%s,%s) to (%s,%s,%s)" %(
tuple(list(params.lower_bounds)+list(params.upper_bounds)))
box = mmtbx.utils.extract_box_around_model_and_map(
xray_structure = xray_structure,
map_data = map_data.as_double(),
box_cushion = params.box_cushion,
selection = selection,
density_select = params.density_select,
threshold = params.density_select_threshold,
get_half_height_width = params.get_half_height_width,
mask_atoms = params.mask_atoms,
soft_mask = params.soft_mask,
soft_mask_radius = params.soft_mask_radius,
mask_atoms_atom_radius = params.mask_atoms_atom_radius,
value_outside_atoms = params.value_outside_atoms,
keep_map_size = params.keep_map_size,
restrict_map_size = params.restrict_map_size,
lower_bounds = params.lower_bounds,
upper_bounds = params.upper_bounds,
extract_unique = params.extract_unique,
chain_type = params.chain_type,
sequence = sequence,
solvent_content = params.solvent_content,
molecular_mass = params.molecular_mass,
resolution = params.resolution,
ncs_object = ncs_object,
symmetry = params.symmetry,
)
ph_box = pdb_hierarchy.select(selection)
ph_box.adopt_xray_structure(box.xray_structure_box)
box.hierarchy=ph_box
if (inputs and # XXX fix or remove this
inputs.crystal_symmetry and inputs.ccp4_map and
inputs.crystal_symmetry.unit_cell().parameters() and
inputs.ccp4_map.unit_cell_parameters ) and (
inputs.crystal_symmetry.unit_cell().parameters() !=
inputs.ccp4_map.unit_cell_parameters):
print >>log,"\nNOTE: Mismatch of unit cell parameters from CCP4 map:"
print >>log,"Unit cell from CCP4 map 'unit cell parameters': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.ccp4_map.unit_cell_parameters)
print >>log,"Unit cell from CCP4 map 'map grid': "+\
"%.1f, %.1f, %.1f, %.1f, %.1f, %.1f)" %tuple(
inputs.crystal_symmetry.unit_cell().parameters())
print >>log,"\nInterpreting this as the 'unit cell parameters' was "+\
"original map \ndimension and 'map grid' is the "+\
"portion actually in the map that was supplied here.\n"
box.unit_cell_parameters_from_ccp4_map=inputs.ccp4_map.unit_cell_parameters
box.unit_cell_parameters_deduced_from_map_grid=\
inputs.crystal_symmetry.unit_cell().parameters()
else:
box.unit_cell_parameters_from_ccp4_map=None
box.unit_cell_parameters_deduced_from_map_grid=None
if box.pdb_outside_box_msg:
print >> log, box.pdb_outside_box_msg
# NOTE: box object is always shifted to place origin at (0,0,0)
# NOTE ON ORIGIN SHIFTS: The shifts are applied locally here. The box
# object is not affected and always has the origin at (0,0,0)
# output_box is copy of box with shift_cart corresponding to the output
# files. Normally this is the same as the original shift_cart. However
# if user has specified a new output origin it will differ.
# For output files ONLY:
# keep_origin==False leave origin at (0,0,0)
# keep_origin==True: we shift everything back to where it was,
# output_origin_grid_units=10,10,10: output origin is at (10,10,10)
# ncs_object is original
# box.ncs_object is shifted by shift_cart
# output_box.ncs_object is shifted back by -new shift_cart
# Additional note on output unit_cell and grid_units.
# The ccp4-style output map can specify the unit cell and grid units
# corresponding to that cell. This can be separate from the origin and
# number of grid points in the map as written. If specified, write these
# out to the output ccp4 map and also use this unit cell for writing
# any output PDB files
from copy import deepcopy
output_box=deepcopy(box) # won't use box below here except to return it
print >>log,"\nBox cell dimensions: (%.2f, %.2f, %.2f) A" %(
box.box_crystal_symmetry.unit_cell().parameters()[:3])
if box.shift_cart:
print>>log,"Working origin moved from grid position of"+\
": (%d, %d, %d) to (0,0,0) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print>>log,"Working origin moved from coordinates of:"+\
" (%.2f, %.2f, %.2f) A to (0,0,0)\n" %(
tuple(-col(box.shift_cart)))
if (params.keep_origin):
print >>log,"\nRestoring original position for output files"
print >>log,"Origin will be at grid position of"+\
": (%d, %d, %d) " %(
tuple(box.origin_shift_grid_units(reverse=True)))
print >>log,\
"\nOutput files will be in same location as original",
if not params.keep_map_size:
print >>log,"just cut out."
else:
print >>log,"keeping entire map"
print >>log,"Note that output maps are only valid in the cut out region.\n"
else:
if origin_to_match:
output_box.shift_cart=shift_cart_for_origin_to_match
if params.output_origin_grid_units:
print >>log,"Output map origin to be shifted to match target"
print >>log, "Placing origin at grid point (%s, %s, %s)" %(
origin_to_match)+"\n"+ \
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
elif box.shift_cart:
output_box.shift_cart=(0,0,0) # not shifting back
print >>log,"Final origin will be at (0,0,0)"
print >>log,\
"Final coordinate shift for output files: (%.2f,%.2f,%.2f) A\n" %(
tuple(col(output_box.shift_cart)-col(box.shift_cart)))
else:
print >>log,\
"\nOutput files are in same location as original and origin "+\
"is at (0,0,0)\n"
ph_output_box_output_location = ph_box.deep_copy()
if output_box.shift_cart: # shift coordinates and NCS back by shift_cart
# NOTE output_box.shift_cart could be different than box.shift_cart if
# there is a target position for the origin and it is not the same as the
# original origin.
sites_cart = output_box.shift_sites_cart_back(
output_box.xray_structure_box.sites_cart())
xrs_offset = ph_output_box_output_location.extract_xray_structure(
crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
).replace_sites_cart(new_sites = sites_cart)
ph_output_box_output_location.adopt_xray_structure(xrs_offset)
if output_box.ncs_object:
output_box.ncs_object=output_box.ncs_object.coordinate_offset(
tuple(-col(output_box.shift_cart)))
shift_back=True
else:
shift_back=False
if params.keep_input_unit_cell_and_grid and \
(input_unit_cell_grid is not None) and \
(input_unit_cell is not None):
params.output_unit_cell=input_unit_cell
params.output_unit_cell_grid=input_unit_cell_grid
print >>log,"Setting output unit cell parameters and unit cell grid to"+\
" match\ninput map file"
if params.output_unit_cell: # Set output unit cell parameters
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=params.output_unit_cell, space_group="P1")
output_unit_cell=output_crystal_symmetry.unit_cell()
print >>log,\
"Output unit cell set to: %.2f, %.2f, %.2f, %.2f, %.2f, %.2f)" %tuple(
output_crystal_symmetry.unit_cell().parameters())
else:
output_crystal_symmetry=None
# ============= Check/set output unit cell grid and cell parameters =======
if params.output_unit_cell_grid or output_crystal_symmetry:
if params.output_unit_cell_grid:
output_unit_cell_grid=params.output_unit_cell_grid
else:
output_unit_cell_grid=output_box.map_box.all()
print >>log,\
"Output unit cell grid set to: (%s, %s, %s)" %tuple(
output_unit_cell_grid)
expected_output_abc=[]
box_spacing=[]
output_spacing=[]
box_abc=output_box.xray_structure_box.\
crystal_symmetry().unit_cell().parameters()[:3]
if output_crystal_symmetry:
output_abc=output_crystal_symmetry.unit_cell().parameters()[:3]
else:
output_abc=[None,None,None]
for a_box,a_output,n_box,n_output in zip(
box_abc,
output_abc,
output_box.map_box.all(),
output_unit_cell_grid):
expected_output_abc.append(a_box*n_output/n_box)
box_spacing.append(a_box/n_box)
if output_crystal_symmetry:
output_spacing.append(a_output/n_output)
else:
output_spacing.append(a_box/n_box)
if output_crystal_symmetry: # make sure it is compatible...
r0=expected_output_abc[0]/output_abc[0]
r1=expected_output_abc[1]/output_abc[1]
r2=expected_output_abc[2]/output_abc[2]
from libtbx.test_utils import approx_equal
if not approx_equal(r0,r1,eps=0.001) or not approx_equal(r0,r2,eps=0.001):
print >>log,"WARNING: output_unit_cell and cell_grid will "+\
"change ratio of grid spacing.\nOld spacings: "+\
"(%.2f, %.2f, %.2f) A " %(tuple(box_spacing))+\
"\nNew spacings: (%.2f, %.2f, %.2f) A \n" %(tuple(output_spacing))
else:
output_abc=expected_output_abc
from cctbx import crystal
output_crystal_symmetry=crystal.symmetry(
unit_cell=list(output_abc)+[90,90,90], space_group="P1")
print >>log, \
"Output unit cell will be: (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f)\n"%(
tuple(output_crystal_symmetry.unit_cell().parameters()))
else:
output_unit_cell_grid = map_data=output_box.map_box.all()
output_crystal_symmetry=output_box.xray_structure_box.crystal_symmetry()
# ========== Done check/set output unit cell grid and cell parameters =====
if write_output_files:
# Write PDB file
if ph_box.overall_counts().n_residues>0:
if(params.output_file_name_prefix is None):
file_name = "%s_box.pdb"%output_prefix
else: file_name = "%s.pdb"%params.output_file_name_prefix
ph_output_box_output_location.write_pdb_file(file_name=file_name,
crystal_symmetry = output_crystal_symmetry)
print >> log, "Writing boxed PDB with box unit cell to %s" %(
file_name)
# Write NCS file if NCS
if output_box.ncs_object and output_box.ncs_object.max_operators()>0:
if(params.output_file_name_prefix is None):
output_symmetry_file = "%s_box.ncs_spec"%output_prefix
else:
output_symmetry_file = "%s.ncs_spec"%params.output_file_name_prefix
output_box.ncs_object.format_all_for_group_specification(
file_name=output_symmetry_file)
print >>log,"\nWriting symmetry to %s" %( output_symmetry_file)
# Write ccp4 map.
if("ccp4" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.ccp4"%output_prefix
else: file_name = "%s.ccp4"%params.output_file_name_prefix
output_box.write_ccp4_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back)
print >> log, "Writing boxed map "+\
"to CCP4 formatted file: %s"%file_name
# Write xplor map. Shift back if keep_origin=True
if("xplor" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.xplor"%output_prefix
else: file_name = "%s.xplor"%params.output_file_name_prefix
output_box.write_xplor_map(file_name=file_name,
output_crystal_symmetry=output_crystal_symmetry,
output_unit_cell_grid=output_unit_cell_grid,
shift_back=shift_back,)
print >> log, "Writing boxed map "+\
"to X-plor formatted file: %s"%file_name
# Write mtz map coeffs. Shift back if keep_origin=True
if("mtz" in params.output_format):
if(params.output_file_name_prefix is None):
file_name = "%s_box.mtz"%output_prefix
else: file_name = "%s.mtz"%params.output_file_name_prefix
print >> log, "Writing map coefficients "+\
"to MTZ file: %s"%file_name
if(map_coeff is not None):
d_min = map_coeff.d_min()
elif params.resolution is not None:
d_min = params.resolution
else:
d_min = maptbx.d_min_from_map(map_data=output_box.map_box,
unit_cell=output_box.xray_structure_box.unit_cell())
output_box.map_coefficients(d_min=d_min,
resolution_factor=params.resolution_factor, file_name=file_name,
shift_back=shift_back)
print >> log
return box